{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T20:32:48Z","timestamp":1790800368926,"version":"4.1.0"},"reference-count":0,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2025,8,6]],"date-time":"2025-08-06T00:00:00Z","timestamp":1754438400000},"content-version":"am","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Molecular compartmentalization is vital for cellular physiology. Spatially-resolved proteomics allows biologists to survey protein composition and dynamics with subcellular resolution. Here we present PEELing, an integrated package and user-friendly web service for analyzing spatially-resolved proteomics data. PEELing assesses data quality using curated or user-defined references, performs cutoff analysis to remove contaminants, connects to databases for functional annotation, and generates data visualizations\u2014providing a streamlined and reproducible workflow to explore spatially-resolved proteomics data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>PEELing and its tutorial are publicly available at https:\/\/peeling.janelia.org\/ (Zenodo DOI: 10.5281\/zenodo.15692517). A Python package of PEELing is available at https:\/\/github.com\/JaneliaSciComp\/peeling\/ (Zenodo DOI: 10.5281\/zenodo.15692434).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>Technical support for PEELing: peeling@janelia.hhmi.org.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf439","type":"journal-article","created":{"date-parts":[[2025,8,12]],"date-time":"2025-08-12T18:02:01Z","timestamp":1755021721000},"source":"Crossref","is-referenced-by-count":7,"title":["PEELing: an integrated and user-centric platform for spatially-resolved proteomics data analysis"],"prefix":"10.1093","author":[{"given":"Xi","family":"Peng","sequence":"first","affiliation":[{"name":"Howard Hughes Medical Institute Janelia Research Campus, , Ashburn, VA 20147,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jody","family":"Clements","sequence":"additional","affiliation":[{"name":"Howard Hughes Medical Institute Janelia Research Campus, , Ashburn, VA 20147,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zuzhi","family":"Jiang","sequence":"additional","affiliation":[{"name":"Howard Hughes Medical Institute Janelia Research Campus, , Ashburn, VA 20147,","place":["United States"]},{"name":"Yuanpei College, Peking University , Beijing, 100871,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuo","family":"Han","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences Key Laboratory of RNA Science and Engineering, Center for Excellence in Molecular Cell Science, , Shanghai, 200031,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephan","family":"Preibisch","sequence":"additional","affiliation":[{"name":"Howard Hughes Medical Institute Janelia Research Campus, , Ashburn, VA 20147,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiefu","family":"Li","sequence":"additional","affiliation":[{"name":"Howard Hughes Medical Institute Janelia Research Campus, , Ashburn, VA 20147,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,8,6]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf439\/63967708\/btaf439.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf439\/63967708\/btaf439.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,8,12]],"date-time":"2025-08-12T18:02:02Z","timestamp":1755021722000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article\/doi\/10.1093\/bioinformatics\/btaf439\/8223222"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,8,6]]},"references-count":0,"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf439","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,8,6]]},"article-number":"btaf439"}}